fish_traits_sum <- fish_traits %>%mutate(across(where(is.numeric), round, 2))## Display the table ----htmltools::tagList(DT::datatable(fish_traits_sum))
traits correlation
Code
M <-cor(numeric_traits[, c(-1)])ggcorrplot::ggcorrplot(M, hc.order =TRUE, type ="lower",lab =TRUE, tl.cex =9, lab_size =3)
Code
# list of species sp_names <-c(rownames(fish_traits))# taxonomic_familiestaxonomic_families <- sp_names %>%as.data.frame() %>%`colnames<-`("species") %>%mutate(family =case_when( species %in%c("Benthosema_glaciale","Ceratoscopelus_maderensis","Diaphus_metopoclampus","Lampanyctus_ater","Lampanyctus_crocodilus","Lampanyctus_macdonaldi","Lobianchia_gemellarii","Myctophum_punctatum","Notoscopelus_bolini","Notoscopelus_kroyeri","Bolinichthys_supralateralis" ) ~"Myctophidae", species %in%c("Borostomias_antarcticus","Chauliodus_sloani","Malacosteus_niger","Melanostomias_bartonbeani","Stomias_boa" ) ~"Stomiidae", species %in%c("Holtbyrnia_anomala","Holtbyrnia_macrops","Maulisia_argipalla","Maulisia_mauli","Maulisia_microlepis","Normichthys_operosus","Searsia_koefoedi","Sagamichthys_schnakenbecki" ) ~"Platytroctidae", species %in%c("Sigmops_bathyphilus","Gonostoma_elongatum") ~"Gonostomatidae", species %in%c("Argyropelecus_hemigymnus","Maurolicus_muelleri","Argyropelecus_olfersii" ) ~"Sternoptychidae", species =="Anoplogaster_cornuta"~"Anoplogastridae", species %in%c("Arctozenus_risso", "Paralepis_coregonoides") ~"Paralepididae", species =="Bathylagus_euryops"~"Bathylagidae", species =="Cyclothone"~"Gonostomatidae", species =="Derichthys_serpentinus"~"Derichthyidae", species =="Eurypharynx_pelecanoides"~"Eurypharyngidae", species =="Evermannella_balbo"~"Evermannellidae", species =="Lestidiops_sphyrenoides"~"Lestidiidae", species =="Melanostigma_atlanticum"~"Zoarcidae", species %in%c("Photostylus_pycnopterus","Xenodermichthys_copei") ~"Alepocephalidae", species =="Serrivomer_beanii"~"Serrivomeridae" ) )%>%mutate(order =case_when( family =="Myctophidae"~"Myctophiformes", family %in%c("Stomiidae","Gonostomatidae", "Sternoptychidae") ~"Stomiiformes", family %in%c("Platytroctidae","Alepocephalidae") ~"Alepocephaliformes", family =="Anoplogastridae"~"Trachichthyiformes", family %in%c("Paralepididae","Evermannellidae","Lestidiidae") ~"Aulopiformes", family =="Bathylagidae"~"Argentiniformes", family %in%c("Derichthyidae","Serrivomeridae") ~"Anguilliformes", family =="Eurypharyngidae"~"Saccopharyngiformes", family =="Zoarcidae"~"Perciformes", ) )
## Summary of the assemblages * species data.frame ----asb_sp_fish_summ <- mFD::asb.sp.summary(asb_sp_w = depth_fish_biomass)asb_sp_fish_occ <- asb_sp_fish_summ$"asb_sp_occ"htmltools::tagList(DT::datatable(asb_sp_fish_occ))
2.2 Computing distances between species based on functional traits
We have non-continuous traits so we use the Gower distance(metric = “gower”) as this method allows traits weighting.
2.3 Building functional spaces and chosing the best one
2.3.1 Computing several multimensional functional spaces and assessing their quality
mFD evaluates the quality of PCoA-based multidimensional spaces according to the deviation between trait-based distances and distances in the functional space (extension of Maire et al. (2015) framework).
2.3.3 Testing the correlation between functional axes and traits
Code
sp_faxes_coord_fish <- fspaces_quality_fish$"details_fspaces"$"sp_pc_coord"# As we have 26 traits we have to split the df to see correlation between functional axes and traits # first set ----fish_traits_1 <- fish_traits%>%select(1:9)fish_tr_faxes <- mFD::traits.faxes.cor(sp_tr = fish_traits_1, sp_faxes_coord = sp_faxes_coord_fish[ , c("PC1", "PC2", "PC3", "PC4")], plot = T)## Print traits with significant effect ----fish_tr_faxes$"tr_faxes_stat"[which(fish_tr_faxes$"tr_faxes_stat"$"p.value"<0.05), ]
trait axis test stat value p.value
1 eye_size PC1 Linear Model r2 0.166 0.0083
2 eye_size PC2 Linear Model r2 0.189 0.0045
4 eye_size PC4 Linear Model r2 0.168 0.0077
5 orbital_length PC1 Linear Model r2 0.405 0.0000
6 orbital_length PC2 Linear Model r2 0.109 0.0346
10 gill_outflow PC2 Linear Model r2 0.476 0.0000
13 oral_gape_surface PC1 Linear Model r2 0.135 0.0181
14 oral_gape_surface PC2 Linear Model r2 0.471 0.0000
18 oral_gape_shape PC2 Linear Model r2 0.163 0.0088
24 oral_gape_position PC4 Linear Model r2 0.243 0.0011
26 lower_jaw_length PC2 Linear Model r2 0.683 0.0000
29 head_length PC1 Linear Model r2 0.325 0.0001
30 head_length PC2 Linear Model r2 0.378 0.0000
34 body_depth PC2 Linear Model r2 0.375 0.0000
35 body_depth PC3 Linear Model r2 0.174 0.0066
Code
## Plot ----fish_tr_faxes$"tr_faxes_plot"
Code
# second set ----fish_traits_2 <- fish_traits%>%select(10:18)fish_tr_faxes_2 <- mFD::traits.faxes.cor(sp_tr = fish_traits_2, sp_faxes_coord = sp_faxes_coord_fish[ , c("PC1", "PC2", "PC3", "PC4")], plot = T)## Print traits with significant effect ----fish_tr_faxes_2$"tr_faxes_stat"[which(fish_tr_faxes_2$"tr_faxes_stat"$"p.value"<0.05), ]
trait axis test stat value p.value
2 pectoral_fin_position PC2 Linear Model r2 0.268 0.0005
5 pectoral_fin_insertion PC1 Linear Model r2 0.283 0.0003
6 pectoral_fin_insertion PC2 Linear Model r2 0.394 0.0000
9 transversal_shape PC1 Linear Model r2 0.116 0.0294
11 transversal_shape PC3 Linear Model r2 0.204 0.0031
14 caudal_throttle_width PC2 Linear Model r2 0.397 0.0000
19 dorsal_fin_insertion PC3 Linear Model r2 0.173 0.0068
23 eye_position PC3 Linear Model r2 0.192 0.0041
32 ventral_photophores PC4 Kruskal-Wallis eta2 0.590 0.0000
33 gland_head PC1 Kruskal-Wallis eta2 0.245 0.0011
Code
## Plot ----fish_tr_faxes_2$"tr_faxes_plot"
Code
# third set ----fish_traits_3 <- fish_traits%>%select(19:26)fish_tr_faxes_3 <- mFD::traits.faxes.cor(sp_tr = fish_traits_3, sp_faxes_coord = sp_faxes_coord_fish[ , c("PC1", "PC2", "PC3", "PC4")], plot = T)## Print traits with significant effect ----fish_tr_faxes_3$"tr_faxes_stat"[which(fish_tr_faxes_3$"tr_faxes_stat"$"p.value"<0.05), ]
Standard Effect Size (SES): to eliminate the influence of species richness on the functional diversity indices (Mouchet et al., 2010). Measures the deviation from the random expectation in standard deviation units
null model frequency: Randomize community data matrix abundances (here biomasss) within species (maintains species occurrence frequency)
FRic Functional Richness: the proportion of functional space filled by species of the studied assemblage, i.e. the volume inside the convex-hull shaping species. To compute FRic the number of species must be at least higher than the number of functional axis + 1.
FDis Functional Dispersion: the biomass weighted deviation of species traits values from the center of the functional space filled by the assemblage i.e. the biomass-weighted mean distance to the biomass-weighted mean trait values of the assemblage.
FDiv Functional Divergence: the proportion of the biomass supported by the species with the most extreme functional traits i.e. the ones located close to the edge of the convex-hull filled by the assemblage.
FEve Functional Evenness: the regularity of biomass distribution in the functional space using the Minimum Spanning Tree linking all species present in the assemblage.
Code
# Calculate functional diversity for the observed data ----obsFD <- mFD::alpha.fd.multidim(sp_faxes_coord = sp_faxes_coord_fish[, c("PC1", "PC2", "PC3", "PC4")],asb_sp_w = depth_fish_biomass,ind_vect =c("fdis", "feve", "fric", "fdiv"),scaling =TRUE,check_input =TRUE,details_returned = F)obsFD_div <- obsFD$functional_diversity_indices# Null model ----# Define the number of replicationsnb_rep <-10# Initialize a list to store results of random functional diversity calculations for each indexindices_names <-colnames(obsFD_div)resultsRandomFD <-list()for (index_name in indices_names) { resultsRandomFD[[index_name]] <-matrix(NA,nrow =nrow(depth_fish_biomass),ncol = nb_rep,dimnames =list(rownames(depth_fish_biomass), paste0("Sim.", 1:nb_rep)) )}# Perform randomization and calculate functional diversity for each replicationfor (rep in1:nb_rep) { randomize_mx <- picante::randomizeMatrix(samp = depth_fish_biomass,null.model ="frequency",iterations =1) simFD_cal <- mFD::alpha.fd.multidim(sp_faxes_coord = sp_faxes_coord_fish[, c("PC1", "PC2", "PC3", "PC4")],asb_sp_w = randomize_mx,ind_vect =c("fdis", "feve", "fric", "fdiv"),scaling =TRUE,check_input =TRUE,details_returned = F ) simFD_div <- simFD_cal$functional_diversity_indicesfor (index_name in indices_names) { simFD_index <- simFD_div[, index_name]# Ensure that simFD_index has the same length as the number of rows in depth_fish_biomassif (length(simFD_index) ==nrow(depth_fish_biomass)) { resultsRandomFD[[index_name]][, rep] <- simFD_index } else {stop(paste("The length of", index_name,"does not match the number of rows in depth_fish_biomass" ) ) } }}# Initialize dataframes to store mean, standard deviation, effect size, and standardized effect sizemeanNullFD <-data.frame(matrix(NA, nrow =nrow(depth_fish_biomass), ncol =length(indices_names)))sdNullFD <-data.frame(matrix(NA, nrow =nrow(depth_fish_biomass), ncol =length(indices_names)))ES_FD <-data.frame(matrix(NA, nrow =nrow(depth_fish_biomass), ncol =length(indices_names)))SES_FD <-data.frame(matrix(NA, nrow =nrow(depth_fish_biomass), ncol =length(indices_names)))# Set column names for the dataframescolnames(meanNullFD) <- indices_namescolnames(sdNullFD) <- indices_namescolnames(ES_FD) <- indices_namescolnames(SES_FD) <- indices_names# Dataframe to store SES values for testing normalitySES_values_reps <-data.frame()# Calculate statistics and SES for each index and store SES in both dataframesfor (index_name in indices_names) {# Calculate mean and standard deviation of null model FD values for each index meanNullFD[, index_name] <-rowMeans(resultsRandomFD[[index_name]], na.rm =TRUE) sdNullFD[, index_name] <-apply(resultsRandomFD[[index_name]], 1, sd, na.rm =TRUE)# Calculate effect size and standardized effect size for each index ES_FD[, index_name] <- obsFD_div[, index_name] - meanNullFD[, index_name] SES_FD[, index_name] <- ES_FD[, index_name] / sdNullFD[, index_name]# Calculate SES for each repetition and add to SES_values_reps dataframefor (rep in1:nb_rep) { SES_repetition <- (resultsRandomFD[[index_name]][, rep] - meanNullFD[, index_name]) / sdNullFD[, index_name] SES_values_reps <-rbind( SES_values_reps,data.frame(depth_layer =rownames(depth_fish_biomass),SES = SES_repetition,index = index_name,repetition =paste0("Rep_", rep) ) ) }}# Combine all results into a single dataframeresults_df <-cbind( obsFD_div,meanNullFD = meanNullFD,sdNullFD = sdNullFD,ES_FD = ES_FD,SES_FD = SES_FD)# Add row namesrownames(results_df) <-rownames(depth_fish_biomass)# Plot ----# Output the results dataframeresults_df_plot <- results_df %>% tibble::rownames_to_column(var ="depth_layer") %>% tidyr::pivot_longer(!depth_layer,values_to ="values",names_to ="indice") %>%mutate(indice = stringr::str_replace(indice, "^SES_", "")) %>%filter(indice %in%c("FD.fric","FD.fdis","FD.feve","FD.fdiv"))results_df_plot$depth_layer <-factor( results_df_plot$depth_layer,levels =c("Epipelagic","Upper mesopelagic","Lower mesopelagic","Bathypelagic" ))results_df_plot$indice <-factor( results_df_plot$indice,levels =c("FD.fric","FD.fdis","FD.fdiv","FD.feve"),labels =c("Functional richness","Functional dispersion","Functional divergence","Functional evenness" ))ggplot(results_df_plot, aes(x = depth_layer, y = values, fill = depth_layer)) +facet_wrap(~indice) +geom_point(size =3, aes(col=depth_layer)) +scale_color_manual(values =c("#FEA520", "#D62246", "#6255B4", "#3C685A")) +scale_fill_manual(values =c("#FEA520", "#D62246", "#6255B4", "#3C685A")) +labs(x ="",y ="Standard Effect Size (SES)") +theme_light() +theme(axis.text.x =element_blank(),strip.text.x =element_text(size =14, color ="black"),strip.background =element_rect(fill ="white"),axis.title =element_text(size =13),axis.text =element_text(size =13)) +guides(col="none", fill="none")
# normality and symetry tests ----test_norm <- SES_values_reps %>% tibble::remove_rownames() %>%filter(index %in%c("fdis", "fdiv", "feve", "fric"))# Compute skewness and Lilliefors tests to check normaltiy and symetry stat_indices <- test_norm %>%group_by(index, depth_layer) %>%summarise(skewness =round(e1071::skewness(SES),2),Lilliefors_pvalue =round(nortest::lillie.test(SES)$p.value,2) )htmltools::tagList(DT::datatable(stat_indices))
the red dashed line = normal distribution
Code
test_norm$depth_layer <-factor( test_norm$depth_layer,levels =c("Epipelagic","Upper mesopelagic","Lower mesopelagic","Bathypelagic" ))# Density plot with normal density overlayggpubr::ggdensity(test_norm, x ="SES", fill ="gray", col ="white") +facet_grid(depth_layer~index, scales ="free") + ggpubr::stat_overlay_normal_density(color ="red", linetype ="dashed", size =1) +theme_light() +labs(title ="Distribution of values of the random communites in compariaosn to the normal distribution",x ="Values", y ="Density")
# # by depth# station_sp <-# rbind(data_biomass_2002_2019, data_biomass_2021_2022) %>%# as.data.frame() %>%# left_join(metadata) %>%# select(species, biomass_sp, volume_filtered, station) %>%# # Divide biomass by the volume filtered at each trawl (g.m3)# mutate(biomass_cpu = (biomass_sp / volume_filtered) * 1000) %>%# select(species, biomass_cpu, station) %>%# replace(is.na(.), 0) %>%# group_by(species, station) %>%# mutate(biomass = sum(biomass_cpu)) %>%# select(-biomass_cpu) %>%# distinct() %>%# tidyr::pivot_wider(names_from = species, values_from = biomass) %>%# replace(is.na(.), 0) %>%# arrange(station) %>%# filter(!station %in% c("H0411", "L0731", "L0736")) %>%# tibble::column_to_rownames(var = "station") %>%# select(order(colnames(.))) %>%# as.matrix()# # # if we want only presence-absence# #station_sp <- replace(station_sp, station_sp > 0, 1)# # # Calculate functional diversity for the observed data ----# obsFD <- mFD::alpha.fd.multidim(# sp_faxes_coord = sp_faxes_coord_fish[, c("PC1", "PC2", "PC3", "PC4")],# asb_sp_w = station_sp,# scaling = TRUE,# check_input = TRUE,# details_returned = F# )# # obsFD_div <- obsFD$functional_diversity_indices# # # Null model ----# # Define the number of replications# nb_rep <- 10# # # Initialize a list to store results of random functional diversity calculations for each index# indices_names <- colnames(obsFD_div)# resultsRandomFD <- list()# # for (index_name in indices_names) {# resultsRandomFD[[index_name]] <- matrix(# NA,# nrow = nrow(station_sp),# ncol = nb_rep,# dimnames = list(rownames(station_sp), paste0("Sim.", 1:nb_rep))# )# }# # # Perform randomization and calculate functional diversity for each replication# for (rep in 1:nb_rep) {# randomize_mx <- picante::randomizeMatrix(samp = station_sp,# null.model = "frequency",# iterations = 1)# # simFD_cal <- mFD::alpha.fd.multidim(# sp_faxes_coord = sp_faxes_coord_fish[, c("PC1", "PC2", "PC3", "PC4")],# asb_sp_w = randomize_mx,# scaling = TRUE,# check_input = TRUE,# details_returned = F# )# # simFD_div <- simFD_cal$functional_diversity_indices# # for (index_name in indices_names) {# simFD_index <- simFD_div[, index_name]# # # Ensure that simFD_index has the same length as the number of rows in station_sp# if (length(simFD_index) == nrow(station_sp)) {# resultsRandomFD[[index_name]][, rep] <- simFD_index# } else {# stop(# paste(# "The length of",# index_name,# "does not match the number of rows in station_sp"# )# )# }# }# }# # # Initialize dataframes to store mean, standard deviation, effect size, and standardized effect size# meanNullFD <-# data.frame(matrix(# NA,# nrow = nrow(station_sp),# ncol = length(indices_names)# ))# sdNullFD <-# data.frame(matrix(# NA,# nrow = nrow(station_sp),# ncol = length(indices_names)# ))# ES_FD <-# data.frame(matrix(# NA,# nrow = nrow(station_sp),# ncol = length(indices_names)# ))# SES_FD <-# data.frame(matrix(# NA,# nrow = nrow(station_sp),# ncol = length(indices_names)# ))# # # Set column names for the dataframes# colnames(meanNullFD) <- indices_names# colnames(sdNullFD) <- indices_names# colnames(ES_FD) <- indices_names# colnames(SES_FD) <- indices_names# # # Calculate statistics for each index# for (index_name in indices_names) {# # Calculate mean and standard deviation of null model FD values for each index# meanNullFD[, index_name] <-# rowMeans(resultsRandomFD[[index_name]], na.rm = TRUE)# sdNullFD[, index_name] <-# apply(resultsRandomFD[[index_name]], 1, sd, na.rm = TRUE)# # # Calculate effect size and standardized effect size for each index# ES_FD[, index_name] <-# obsFD_div[, index_name] - meanNullFD[, index_name]# SES_FD[, index_name] <-# ES_FD[, index_name] / sdNullFD[, index_name]# }# # # Combine all results into a single dataframe# results_df <- cbind(# obsFD_div,# meanNullFD = meanNullFD,# sdNullFD = sdNullFD,# ES_FD = ES_FD,# SES_FD = SES_FD# )# # # Add row names# rownames(results_df) <- rownames(station_sp)# # # Plot ----# # Output the results dataframe# results_df_plot <- results_df %>%# tibble::rownames_to_column(var = "station") %>%# inner_join(metadata %>% select(station, depth), by = "station") %>%# mutate(# depth_layer = case_when(# between(depth, 0, 174) ~ "Epipelagic",# between(depth, 175, 699) ~ "Upper mesopelagic",# between(depth, 700, 999) ~ "Lower mesopelagic",# between(depth, 1000, 2000) ~ "Bathypelagic"# )# ) %>%# select(-station) %>%# tidyr::pivot_longer(!c(depth, depth_layer),# values_to = "values",# names_to = "indice") %>%# mutate(indice = stringr::str_replace(indice, "^SES_", "")) %>%# filter(indice %in% c("FD.fric",# "FD.fdis",# "FD.feve",# "FD.fdiv"))# # results_df_plot$depth_layer <- factor(# results_df_plot$depth_layer,# levels = c(# "Epipelagic",# "Upper mesopelagic",# "Lower mesopelagic",# "Bathypelagic"# )# )# results_df_plot$indice <- factor(# results_df_plot$indice,# levels = c("FD.fric",# "FD.fdis",# "FD.fdiv",# "FD.feve"),# labels = c(# "Functional richness",# "Functional dispersion",# "Functional divergence",# "Functional evenness"# )# )# # ggplot(results_df_plot, aes(x = depth_layer, y = values, fill = depth_layer)) +# facet_wrap(~indice, scales = "free") +# geom_point(alpha = 0.5, size = 1, position = position_jitter(width = 0.2), aes(col=depth_layer)) +# geom_boxplot(alpha = 0.1, outlier.shape = NA, width = 0.5, aes(col=depth_layer, fill=depth_layer))+# scale_color_manual(values = c("#FEA520", "#D62246", "#6255B4", "#3C685A")) +# scale_fill_manual(values = c("#FEA520", "#D62246", "#6255B4", "#3C685A")) +# labs(# x = "",# y = "Standard Effect Size (SES)") +# theme_light() +# theme(axis.text.x = element_blank(),# strip.text.x = element_text(size = 14, color = "black"),# strip.background = element_rect(fill = "white"),# axis.title = element_text(size = 13),# axis.text = element_text(size = 13))+# geom_hline(yintercept = 1.96, linetype = "dashed", color = "gray50", linewidth = 0.8)+# geom_hline(yintercept = -1.96, linetype = "dashed", color = "gray50", linewidth = 0.8)+# guides(col="none", fill="none")#ggsave("SES_indices_1000.png", path = "figures", dpi = 700, height = 7, width = 9)
7. Nouveaux tests modèles nuls
7.1. Model “richness” by depth layer
Model of randomization = “richness” & by depth layer la biomasse des espèces est donc randomisée par couche de profondeur (seules les espèces présentes dans la couche de profondeur). Dans ce cas, je n’obtiens pas de valeurs de SES pour la richesse fonctionelle car cet indice ne prend pas en compte la biomasse des espèces, seulement leur présence et donc j’obtiens les mêmes valeurs de Functional richness pour les valeurs observées et les valeurs simulées donc les valeurs de SES sont toujours = 0 (que les valeurs de biomasses soient randomisées ou pas ça ne change rien)
Code
# Calculate functional diversity for the observed data ----obsFD <- mFD::alpha.fd.multidim(sp_faxes_coord = sp_faxes_coord_fish[, c("PC1", "PC2", "PC3", "PC4")],asb_sp_w = depth_fish_biomass,ind_vect =c("fdis", "feve", "fdiv"),scaling =TRUE,check_input =TRUE,details_returned =FALSE)obsFD_div <- obsFD$functional_diversity_indices# Null model ----# Define the number of replicationsnb_rep <-10null_model_used <-"richness"# Initialize a list to store results of random functional diversity calculations for each indexindices_names <-colnames(obsFD_div)resultsRandomFD <-list()randomized_matrices <-list() # List to store randomized matricesfor (index_name in indices_names) { resultsRandomFD[[index_name]] <-matrix(NA,nrow =nrow(depth_fish_biomass),ncol = nb_rep,dimnames =list(rownames(depth_fish_biomass), paste0("Sim.", 1:nb_rep)) )}# Perform randomization and calculate functional diversity for each depth layerfor (depth_layer inunique(rownames(depth_fish_biomass))) {# Subset biomass matrix for the current depth layer sub_biomass <- depth_fish_biomass[rownames(depth_fish_biomass) == depth_layer, , drop =FALSE]# Filter species with biomass > 0 sub_biomass <- sub_biomass[, colSums(sub_biomass) >0, drop =FALSE]for (rep in1:nb_rep) { randomize_mx <- picante::randomizeMatrix(samp = sub_biomass,null.model = null_model_used,iterations =1 )# Store the randomized matrix randomized_matrices[[paste0(depth_layer, "_Rep_", rep)]] <- randomize_mx simFD_cal <- mFD::alpha.fd.multidim(sp_faxes_coord = sp_faxes_coord_fish[, c("PC1", "PC2", "PC3", "PC4")],asb_sp_w = randomize_mx,ind_vect =c("fdis", "feve", "fdiv"),scaling =TRUE,check_input =TRUE,details_returned =FALSE ) simFD_div <- simFD_cal$functional_diversity_indicesfor (index_name in indices_names) { simFD_index <- simFD_div[, index_name]if (length(simFD_index) ==nrow(sub_biomass)) { resultsRandomFD[[index_name]][rownames(sub_biomass), rep] <- simFD_index } else {stop(paste("The length of", index_name,"does not match the number of rows in sub_biomass for depth layer", depth_layer ) ) } } }}# Initialize dataframes to store mean, standard deviation, effect size, and standardized effect sizemeanNullFD <-data.frame(matrix(NA, nrow =nrow(depth_fish_biomass), ncol =length(indices_names)))sdNullFD <-data.frame(matrix(NA, nrow =nrow(depth_fish_biomass), ncol =length(indices_names)))ES_FD <-data.frame(matrix(NA, nrow =nrow(depth_fish_biomass), ncol =length(indices_names)))SES_FD <-data.frame(matrix(NA, nrow =nrow(depth_fish_biomass), ncol =length(indices_names)))# Set column names for the dataframescolnames(meanNullFD) <- indices_namescolnames(sdNullFD) <- indices_namescolnames(ES_FD) <- indices_namescolnames(SES_FD) <- indices_names# Dataframe to store SES values for testing normalitySES_values_reps <-data.frame()# Calculate statistics and SES for each index and store SES in both dataframesfor (index_name in indices_names) {# Calculate mean and standard deviation of null model FD values for each index meanNullFD[, index_name] <-rowMeans(resultsRandomFD[[index_name]], na.rm =TRUE) sdNullFD[, index_name] <-apply(resultsRandomFD[[index_name]], 1, sd, na.rm =TRUE)# Calculate effect size and standardized effect size for each index ES_FD[, index_name] <- obsFD_div[, index_name] - meanNullFD[, index_name] SES_FD[, index_name] <- ES_FD[, index_name] / sdNullFD[, index_name]# Calculate SES for each repetition and add to SES_values_reps dataframefor (rep in1:nb_rep) { SES_repetition <- (resultsRandomFD[[index_name]][, rep] - meanNullFD[, index_name]) / sdNullFD[, index_name] SES_values_reps <-rbind( SES_values_reps,data.frame(depth_layer =rownames(depth_fish_biomass),SES = SES_repetition,index = index_name,repetition =paste0("Rep_", rep) ) ) }}# Combine all results into a single dataframeresults_df <-cbind( obsFD_div,meanNullFD = meanNullFD,sdNullFD = sdNullFD,ES_FD = ES_FD,SES_FD = SES_FD)# Add row namesrownames(results_df) <-rownames(depth_fish_biomass)# Plot ----# Output the results dataframeresults_df_plot <- results_df %>% tibble::rownames_to_column(var ="depth_layer") %>% tidyr::pivot_longer(!depth_layer,values_to ="values",names_to ="indice") %>%filter(indice %in%c("SES_FD.fdis","SES_FD.fdiv","SES_FD.feve"))results_df_plot$depth_layer <-factor( results_df_plot$depth_layer,levels =c("Epipelagic","Upper mesopelagic","Lower mesopelagic","Bathypelagic" ))results_df_plot$indice <-factor( results_df_plot$indice,levels =c("SES_FD.fdis","SES_FD.fdiv","SES_FD.feve"),labels =c("Functional dispersion","Functional divergence","Functional evenness" ))ggplot(results_df_plot, aes(x = depth_layer, y = values, fill = depth_layer)) +facet_wrap(~indice, ncol=2) +geom_point(size =3, aes(col = depth_layer)) +scale_color_manual(values =c("#FEA520", "#D62246", "#6255B4", "#3C685A")) +scale_fill_manual(values =c("#FEA520", "#D62246", "#6255B4", "#3C685A")) +labs(x ="",y ="Standard Effect Size (SES)",title =paste("nb_rep =", nb_rep, "| Model =", null_model_used) ) +theme_light() +ylim(c(-3,3))+theme(axis.text.x =element_blank(),strip.text.x =element_text(size =14, color ="black"),strip.background =element_rect(fill ="white"),axis.title =element_text(size =13),axis.text =element_text(size =13) ) +guides(col ="none", fill ="none")
# normality and symetry tests ----test_norm <- SES_values_reps %>% tibble::remove_rownames() %>%filter(index %in%c("fdis", "fdiv", "feve"))# Compute skewness and Lilliefors tests to check normality and symmetry stat_indices <- test_norm %>%group_by(index, depth_layer) %>%summarise(skewness =round(e1071::skewness(SES),2),Lilliefors_pvalue =round(nortest::lillie.test(SES)$p.value,2) )htmltools::tagList(DT::datatable(stat_indices))
7.2. Model “frequency” all the community
est-ce que chaque assemblage est + ou - riche fonctionnellment par rapport à l’ensemble des espèces potentiellement présentes au sein de la communauté (donc matrice randomisée sur l’ensemble des couches)
Code
# Calculate functional diversity for the observed data ----obsFD <- mFD::alpha.fd.multidim(sp_faxes_coord = sp_faxes_coord_fish[, c("PC1", "PC2", "PC3", "PC4")],asb_sp_w = depth_fish_biomass,ind_vect =c("fric"),scaling =TRUE,check_input =TRUE,details_returned = F)obsFD_div <- obsFD$functional_diversity_indices# Null model ----# Define the number of replicationsnb_rep <-10# Initialize a list to store results of random functional diversity calculations for each indexindices_names <-colnames(obsFD_div)resultsRandomFD <-list()for (index_name in indices_names) { resultsRandomFD[[index_name]] <-matrix(NA,nrow =nrow(depth_fish_biomass),ncol = nb_rep,dimnames =list(rownames(depth_fish_biomass), paste0("Sim.", 1:nb_rep)) )}# Perform randomization and calculate functional diversity for each replicationfor (rep in1:nb_rep) { randomize_mx <- picante::randomizeMatrix(samp = depth_fish_biomass,null.model ="frequency",iterations =1) simFD_cal <- mFD::alpha.fd.multidim(sp_faxes_coord = sp_faxes_coord_fish[, c("PC1", "PC2", "PC3", "PC4")],asb_sp_w = randomize_mx,ind_vect =c("fric"),scaling =TRUE,check_input =TRUE,details_returned = F ) simFD_div <- simFD_cal$functional_diversity_indicesfor (index_name in indices_names) { simFD_index <- simFD_div[, index_name]# Ensure that simFD_index has the same length as the number of rows in depth_fish_biomassif (length(simFD_index) ==nrow(depth_fish_biomass)) { resultsRandomFD[[index_name]][, rep] <- simFD_index } else {stop(paste("The length of", index_name,"does not match the number of rows in depth_fish_biomass" ) ) } }}# Initialize dataframes to store mean, standard deviation, effect size, and standardized effect sizemeanNullFD <-data.frame(matrix(NA, nrow =nrow(depth_fish_biomass), ncol =length(indices_names)))sdNullFD <-data.frame(matrix(NA, nrow =nrow(depth_fish_biomass), ncol =length(indices_names)))ES_FD <-data.frame(matrix(NA, nrow =nrow(depth_fish_biomass), ncol =length(indices_names)))SES_FD <-data.frame(matrix(NA, nrow =nrow(depth_fish_biomass), ncol =length(indices_names)))# Set column names for the dataframescolnames(meanNullFD) <- indices_namescolnames(sdNullFD) <- indices_namescolnames(ES_FD) <- indices_namescolnames(SES_FD) <- indices_names# Dataframe to store SES values for testing normalitySES_values_reps <-data.frame()# Calculate statistics and SES for each index and store SES in both dataframesfor (index_name in indices_names) {# Calculate mean and standard deviation of null model FD values for each index meanNullFD[, index_name] <-rowMeans(resultsRandomFD[[index_name]], na.rm =TRUE) sdNullFD[, index_name] <-apply(resultsRandomFD[[index_name]], 1, sd, na.rm =TRUE)# Calculate effect size and standardized effect size for each index ES_FD[, index_name] <- obsFD_div[, index_name] - meanNullFD[, index_name] SES_FD[, index_name] <- ES_FD[, index_name] / sdNullFD[, index_name]# Calculate SES for each repetition and add to SES_values_reps dataframefor (rep in1:nb_rep) { SES_repetition <- (resultsRandomFD[[index_name]][, rep] - meanNullFD[, index_name]) / sdNullFD[, index_name] SES_values_reps <-rbind( SES_values_reps,data.frame(depth_layer =rownames(depth_fish_biomass),SES = SES_repetition,index = index_name,repetition =paste0("Rep_", rep) ) ) }}# Combine all results into a single dataframeresults_df <-cbind( obsFD_div,meanNullFD = meanNullFD,sdNullFD = sdNullFD,ES_FD = ES_FD,SES_FD = SES_FD)# Add row namesrownames(results_df) <-rownames(depth_fish_biomass)# Plot ----# Output the results dataframeresults_df_plot <- results_df %>% tibble::rownames_to_column(var ="depth_layer") %>% tidyr::pivot_longer(!depth_layer,values_to ="values",names_to ="indice") %>%filter(indice %in%c("SES_FD.fric"))results_df_plot$depth_layer <-factor( results_df_plot$depth_layer,levels =c("Epipelagic","Upper mesopelagic","Lower mesopelagic","Bathypelagic" ))results_df_plot$indice <-factor( results_df_plot$indice,levels =c("SES_FD.fric"),labels =c("Functional richness" ))ggplot(results_df_plot, aes(x = depth_layer, y = values, fill = depth_layer)) +facet_wrap(~indice) +geom_point(size =3, aes(col=depth_layer)) +scale_color_manual(values =c("#FEA520", "#D62246", "#6255B4", "#3C685A")) +scale_fill_manual(values =c("#FEA520", "#D62246", "#6255B4", "#3C685A")) +labs(x ="",y ="Standard Effect Size (SES)") +theme_light() +theme(axis.text.x =element_blank(),strip.text.x =element_text(size =14, color ="black"),strip.background =element_rect(fill ="white"),axis.title =element_text(size =13),axis.text =element_text(size =13)) +guides(col="none", fill="none")
# normality and symmetry tests ----test_norm <- SES_values_reps %>% tibble::remove_rownames() %>%filter(index %in%c("fric"))# Compute skewness and Lilliefors tests to check normality and symmetry stat_indices <- test_norm %>%summarise(skewness =round(e1071::skewness(SES),2),Lilliefors_pvalue =round(nortest::lillie.test(SES)$p.value,2) )htmltools::tagList(DT::datatable(stat_indices))
8. dbFD package
Code
# Load required librarieslibrary(mFD)library(tibble)library(tidyr)library(ggplot2)library(tidyverse)library(FD)library(ade4)library(geometry)source("R/Anik/sp_tr_en_tr_cat.R") # Load datadepth_fish_biomass <-read.csv(here::here("data", "depth_fish_biomass.csv"), row.names =1, sep =";", dec =".")fish_traits <-read.csv(here::here("data", "fish_traits.csv"), row.names =1, sep =";", dec =".")# Convert character traits to factorfish_traits <- fish_traits %>%mutate(across(where(is.character), as.factor))# Function to randomize traits while preserving factor levelsrandomize_traits <-function(traits_mat) { randomized_mat <- traits_matfor (trait incolnames(traits_mat)) {if (is.factor(traits_mat[[trait]])) { randomized_mat[[trait]] <-factor(sample(traits_mat[[trait]], replace =FALSE), levels =levels(traits_mat[[trait]])) } else { randomized_mat[[trait]] <-sample(traits_mat[[trait]], replace =FALSE) } }return(randomized_mat)}# Number of simulationsn_simulations <-99# Depth layersdepth_layers <-rownames(depth_fish_biomass)# Liste des indices à calculerindices <-c("FRic", "FDis", "RaoQ", "FEve", "FDiv") # Matrices pour stocker les résultats observés et simulésdbFD_result_obs <-matrix(NA, nrow =length(depth_layers), ncol =length(indices), dimnames =list(depth_layers, indices))dbFD_result_sim <-array(NA, dim =c(length(depth_layers), n_simulations, length(indices)), dimnames =list(depth_layers, paste0("Sim.", 1:n_simulations), indices))# Boucle sur chaque couche de profondeurfor (layer in depth_layers) {# Sélectionner les espèces présentes species_in_layer <-colnames(depth_fish_biomass)[depth_fish_biomass[layer, ] >0]# Filtrer les traits et retirer les colonnes constantes traits_layer <- fish_traits[species_in_layer, , drop =FALSE] %>%select(where(~length(unique(.)) >1)) # Skip si aucun trait variableif (ncol(traits_layer) ==0) next# Formatage correct de biomass_layer avec la couche de profondeur en rownames biomass_layer <-matrix(as.numeric(depth_fish_biomass[layer, species_in_layer, drop =FALSE]), nrow =1, dimnames =list(layer, species_in_layer))# Calcul des indices observés avec dbFD dbFD_result <-dbFD(x = traits_layer, w.abun =TRUE, m =4, a = biomass_layer)# Stockage des valeurs observées dbFD_result_obs[layer, "FRic"] <- dbFD_result$FRic dbFD_result_obs[layer, "FDis"] <- dbFD_result$FDis dbFD_result_obs[layer, "RaoQ"] <- dbFD_result$RaoQ dbFD_result_obs[layer, "FEve"] <- dbFD_result$FEve dbFD_result_obs[layer, "FDiv"] <- dbFD_result$FDiv # Simulations pour chaque couchefor (sim in1:n_simulations) { randomized_traits <-randomize_traits(traits_layer) dbFD_sim_result <-dbFD(x = randomized_traits, w.abun =TRUE, m =4, a = biomass_layer)# Stockage des valeurs simulées dbFD_result_sim[layer, sim, "FRic"] <- dbFD_sim_result$FRic dbFD_result_sim[layer, sim, "FDis"] <- dbFD_sim_result$FDis dbFD_result_sim[layer, sim, "RaoQ"] <- dbFD_sim_result$RaoQ dbFD_result_sim[layer, sim, "FEve"] <- dbFD_sim_result$FEve dbFD_result_sim[layer, sim, "FDiv"] <- dbFD_sim_result$FDiv # Ajout de FDiv } }
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.5592442
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3799976
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4047834
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3962031
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3991085
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3828376
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4053748
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4023284
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3902178
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4048104
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.404792
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3766959
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3911287
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3862699
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3746401
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4136035
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3775433
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3810074
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3963843
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4042523
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3887518
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3863863
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4025891
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3947365
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3848704
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4191625
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3971385
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3885376
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3922654
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4083638
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3846286
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3883045
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3824085
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3812503
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3802494
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3921416
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3648752
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3843455
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3861762
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3908481
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3941098
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4051832
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3912241
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3852661
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3893313
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.390102
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3765947
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4147487
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4130153
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.379507
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3951045
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3989288
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.408112
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3834656
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3869277
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3966596
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3965808
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4003627
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3802167
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4047851
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.398189
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3843179
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3983072
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3886053
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3886593
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.418399
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3814718
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3824985
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3984591
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3822724
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3933469
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4031128
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.386262
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4006911
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4096291
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3956703
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3807992
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.426164
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4013098
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4092845
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4040044
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3925745
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3946399
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4074047
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4036128
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3957328
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3803934
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3903117
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4131318
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3939651
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3690823
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3803823
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3818765
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3965596
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4026739
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3814306
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3812129
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3920822
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3938952
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 23 PCoA axes (out of 27 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3993839
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.5137392
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3467765
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3516411
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3525279
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3521166
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.34967
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3554568
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3504907
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.350101
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.353793
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3578851
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3665791
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3630778
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3538758
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.355325
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.356775
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3586342
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3592159
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3576532
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3564283
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3575672
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3626749
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3492546
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3469299
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3655509
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3423784
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3492245
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.340173
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3570512
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3611932
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3591562
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.34425
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3577655
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3509508
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3511162
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3361061
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3460557
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3603158
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3590955
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.365476
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3563707
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3771853
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3594326
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3400072
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3445086
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3412778
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3671466
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3530853
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3570254
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3504424
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3587586
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3576827
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3475516
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3637498
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3687818
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3711291
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3541053
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3409258
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3428169
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3426542
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3471379
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3702341
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3465523
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3513077
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3639999
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3479381
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3513193
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3386697
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.337281
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3479238
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3581211
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.343825
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3562197
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3567356
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.350483
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3603851
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3514495
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3548373
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3645224
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3343205
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3500958
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3482274
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3518863
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3560483
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3564165
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3589606
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3663374
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3468569
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.342982
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3346327
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3586066
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3421528
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3343921
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3764966
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.360192
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3430119
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3496068
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.355775
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3501236
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 36 PCoA axes (out of 40 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.355106
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.5874194
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4277026
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4282582
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3872469
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4032471
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4220621
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4144922
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.413735
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4123191
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3926239
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4132
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4079302
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4165124
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.419801
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4112991
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4200175
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3797622
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4133844
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4223836
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4156014
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4306093
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3980171
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4101516
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4081835
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4277438
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4026551
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4353471
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4048388
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3955545
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4236829
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4208463
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4003079
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3834448
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4093516
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3971437
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4023392
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3983048
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4260995
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4059951
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.443168
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4179811
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4116542
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4149313
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3841824
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4025239
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.398978
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3948201
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3803618
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3930186
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4073367
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4047921
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4142515
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4301497
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4047151
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4209804
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.417193
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4224111
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4116267
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4028546
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4138229
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4115594
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4125066
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4065058
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.403397
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4145133
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4014347
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4089572
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3775633
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4158956
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4160706
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4073355
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3972817
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.408401
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4339081
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4215362
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3968654
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4216986
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4124716
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4163648
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3852476
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4170657
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4082208
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3770814
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4143587
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4052251
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4189482
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4432004
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4232666
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4103569
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4111617
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4079408
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4101993
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4117218
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.411363
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3803408
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4102198
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4108237
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3929971
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.4054456
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 19 PCoA axes (out of 23 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3944532
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.535749
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3698298
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3878549
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3743685
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3899748
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3790223
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3596004
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3791912
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3592363
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3763115
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3520795
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3727414
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3922666
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3809939
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.356703
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.374572
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3576206
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3669458
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3784061
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3765365
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3625192
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3696057
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.369098
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3862997
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3719632
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3731989
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3531653
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3702458
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3783684
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3681174
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3559033
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3736394
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3739289
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3640517
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3625299
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.372615
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3514366
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3739934
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3852696
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3579496
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3825319
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.38281
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3787374
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3597412
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3746578
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3573191
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3544962
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3399768
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3656062
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3640283
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3930996
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3974442
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.388421
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3489135
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3571949
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3711707
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.361986
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3876442
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3600762
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3716178
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3905203
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3573766
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3620874
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3788972
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3694852
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3614896
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3729697
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3734026
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3717414
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3789075
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.37273
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3693676
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3811557
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.374026
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3742018
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3915909
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3696418
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3886588
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3561602
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3749333
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3658189
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3611956
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3519547
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3608021
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3664899
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3803946
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3661657
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3691335
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3794733
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3651937
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3503887
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3538472
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3612382
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3878854
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3594247
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3626944
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3674468
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3776421
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.365041
Species x species distance matrix was not Euclidean. 'sqrt' correction was applied.
FRic: Dimensionality reduction was required. The last 27 PCoA axes (out of 31 in total) were removed.
FRic: Quality of the reduced-space representation (based on corrected distance matrix) = 0.3600584
Code
# Calcul du SES (Standardized Effect Size) pour chaque indice séparémentSES_results <-data.frame(depth_layer =rownames(dbFD_result_obs))for (index in indices) { meanNullFD <-rowMeans(dbFD_result_sim[, , index], na.rm =TRUE) sdNullFD <-apply(dbFD_result_sim[, , index], 1, sd, na.rm =TRUE) SES_results[[index]] <- (dbFD_result_obs[, index] - meanNullFD) / sdNullFD}# Transformation des résultats pour ggplotresults_df <-pivot_longer(SES_results, cols =-depth_layer, names_to ="Index", values_to ="SES_FD")# Convertir depth_layer en facteur pour le bon ordreresults_df$depth_layer <-factor(results_df$depth_layer, levels =c("Epipelagic", "Upper mesopelagic", "Lower mesopelagic", "Bathypelagic"))# Plot ggplot(results_df, aes(x = depth_layer, y = SES_FD, color = depth_layer)) +geom_point(size =3) +geom_hline(yintercept =c(1.96, -1.96), linetype ="dashed", color ="gray50") +scale_color_manual(values =c("#FEA520", "#D62246", "#6255B4", "#3C685A")) +labs(x ="", y ="Standard Effect Size (SES)") +facet_wrap(~Index) +theme_light() +theme(axis.text.x =element_blank())